Intelligent Word Embeddings of Free-Text Radiology Reports

Radiology reports are a rich resource for advancing deep learning applications in medicine by leveraging the large volume of data continuously being updated, integrated, and shared. However, there are significant challenges as well, largely due to the ambiguity and subtlety of natural language. We propose a hybrid strategy that combines semantic-dictionary mapping and word2vec modeling for creating dense vector embeddings of free-text radiology reports. Our method leverages the benefits of both semantic-dictionary mapping as well as unsupervised learning. Using the vector representation, we automatically classify the radiology reports into three classes denoting confidence in the diagnosis of intracranial hemorrhage by the interpreting radiologist. We performed experiments with varying hyperparameter settings of the word embeddings and a range of different classifiers. Best performance achieved was a weighted precision of 88% and weighted recall of 90%. Our work offers the potential to leverage unstructured electronic health record data by allowing direct analysis of narrative clinical notes.Comment: AMIA Annual Symposium 201

The non-vanishing effect of detuning errors in dynamical decoupling based quantum sensing experiments

Characteristic dips appear in the coherence traces of a probe qubit when dynamical decoupling (DD) is applied in synchrony with the precession of target nuclear spins, forming the basis for nanoscale nuclear magnetic resonance (NMR). The frequency of the microwave control pulses is chosen to match the qubit transition but this can be detuned from resonance by experimental errors, hyperfine coupling intrinsic to the qubit, or inhomogeneous broadening. The detuning acts as an additional static field which is generally assumed to be completely removed in Hahn echo and DD experiments. Here we demonstrate that this is not the case in the presence of finite pulse-durations, where a detuning can drastically alter the coherence response of the probe qubit, with important implications for sensing applications. Using the electronic spin associated with a nitrogen-vacancy centre in diamond as a test qubit system, we analytically and experimentally study the qubit coherence response under CPMG and XY8 dynamical decoupling control schemes in the presence of finite pulse-durations and static detunings. Most striking is the splitting of the NMR resonance under CPMG, whereas under XY8 the amplitude of the NMR signal is modulated. Our work shows that the detuning error must not be neglected when extracting data from quantum sensor coherence traces

Role of graft oversizing in the fixation strength of barbed endovascular grafts

PurposeThe role of endovascular graft oversizing on risk of distal graft migration following endovascular aneurysm repair for abdominal aortic aneurysm is poorly understood. A controlled in vitro investigation of the role of oversizing in graft-aorta attachment strength for endovascular grafts (EVGs) with barbs was performed.MethodsBarbed stent grafts (N = 20) with controlled graft oversizing varying from 4-45% were fabricated while maintaining other design variables unchanged. A flow loop with physiological flow characteristics and a biosynthetic aortic aneurysm phantom (synthetic aneurysm model with a bovine aortic neck) were developed. The stent grafts were deployed into the aortic neck of the bio-synthetic aortic aneurysm phantom under realistic flow conditions. Computed tomography imaging of the graft-aorta complex was used to document attachment characteristics such as graft apposition, number of barbs penetrated, and penetration depth and angle. The strength of graft attachment to the aortic neck was assessed using mechanical pullout testing. Stent grafts were categorized into four groups based on oversizing: 4-10%; 11-20%; 21-30%; and greater than 30% oversizing.ResultsPullout force, a measure of post-deployment fixation strength was not different between 4-10% (6.23 ± 1.90 N), 11-20% (6.25 ± 1.84 N) and 20-30% (5.85 ± 1.89 N) groups, but significantly lower for the group with greater than 30% oversizing (3.67 ± 1.41 N). Increasing oversizing caused a proportional decrease in the number of barbs penetrating the aortic wall (correlation = −0.83). Of the 14 barbs available in the stent graft, 89% of the barbs (12.5 of 14 on average) penetrated the aortic wall in the 4-10% oversizing group while only 38% (5.25 of 14) did for the greater than 30% group (P < .001). Also, the stent grafts with greater than 30% oversizing showed significantly poorer apposition characteristics such as eccentric compression or folding of the graft perimeter. The number and depth of barb penetration were found to be positively correlated to pullout force.ConclusionGreater than 30% graft oversizing affects both barb penetration and graft apposition adversely resulting in a low pullout force in this in vitro model. Barbed stent grafts with excessive oversizing are likely to result in poor fixation and increased risk of migration.Clinical RelevanceMigration of the endovascular grafts in abdominal aortic aneurysm (AAA) patients continues to be a cause of long-term complication in patients. This study is an assessment of the role of graft oversizing, a key variable chosen by the physician, on the fixation strength of these implants to the parent aorta. The findings suggest caution when choosing stent grafts that are excessively oversized

Polymer Parametrised Field Theory

Free scalar field theory on 2 dimensional flat spacetime, cast in diffeomorphism invariant guise by treating the inertial coordinates of the spacetime as dynamical variables, is quantized using LQG type `polymer' representations for the matter field and the inertial variables. The quantum constraints are solved via group averaging techniques and, analogous to the case of spatial geometry in LQG, the smooth (flat) spacetime geometry is replaced by a discrete quantum structure. An overcomplete set of Dirac observables, consisting of (a) (exponentials of) the standard free scalar field creation- annihilation modes and (b) canonical transformations corresponding to conformal isometries, are represented as operators on the physical Hilbert space. None of these constructions suffer from any of the `triangulation' dependent choices which arise in treatments of LQG. In contrast to the standard Fock quantization, the non- Fock nature of the representation ensures that the algebra of conformal isometries as well as that of spacetime diffeomorphisms are represented in an anomaly free manner. Semiclassical states can be analysed at the gauge invariant level. It is shown that `physical weaves' necessarily underly such states and that such states display semiclassicality with respect to, at most, a countable subset of the (uncountably large) set of observables of type (a). The model thus offers a fertile testing ground for proposed definitions of quantum dynamics as well as semiclassical states in LQG.Comment: 44 pages, no figure

Kondo Effect and Surface-State Electrons

We have used low temperature scanning tunneling spectroscopy and atomic manipulation to study the role of surface-state electrons in the Kondo effect of an isolated cobalt atom adsorbed on Ag(111). We show that the observed Kondo signature remains unchanged in close proximity of a monoatomic step, where the local density of states of the surface-state electrons is strongly perturbed. This result indicates a minor role for surface-state electrons in the Kondo effect of cobalt, compared to bulk electrons. A possible explanation for our findings is presented.Comment: 4 pages, 4 figures, ACSIN-7 proceeding

Quantification and expert evaluation of evidence for chemopredictive biomarkers to personalize cancer treatment.

Predictive biomarkers have the potential to facilitate cancer precision medicine by guiding the optimal choice of therapies for patients. However, clinicians are faced with an enormous volume of often-contradictory evidence regarding the therapeutic context of chemopredictive biomarkers.We extensively surveyed public literature to systematically review the predictive effect of 7 biomarkers claimed to predict response to various chemotherapy drugs: ERCC1-platinums, RRM1-gemcitabine, TYMS-5-fluorouracil/Capecitabine, TUBB3-taxanes, MGMT-temozolomide, TOP1-irinotecan/topotecan, and TOP2A-anthracyclines. We focused on studies that investigated changes in gene or protein expression as predictors of drug sensitivity or resistance. We considered an evidence framework that ranked studies from high level I evidence for randomized controlled trials to low level IV evidence for pre-clinical studies and patient case studies.We found that further in-depth analysis will be required to explore methodological issues, inconsistencies between studies, and tumor specific effects present even within high evidence level studies. Some of these nuances will lend themselves to automation, others will require manual curation. However, the comprehensive cataloging and analysis of dispersed public data utilizing an evidence framework provides a high level perspective on clinical actionability of these protein biomarkers. This framework and perspective will ultimately facilitate clinical trial design as well as therapeutic decision-making for individual patients

Theory of STM Spectroscopy of Kondo Ions on Metal Surfaces

The conduction electron density of states nearby a single magnetic impurity, as measured recently by scanning tunneling microscopy (STM), is calculated. It is shown that the Kondo effect induces a narrow Fano resonance as an intrinsic feature in the conduction electron density of states. The line shape varies with the distance between STM tip and impurity, in qualitative agreement with experiments, and is sensitive to details of the band structure. For a Co impurity the experimentally observed width and shift of the Kondo resonance are in accordance with those obtained from a combination of band structure and strongly correlated calculations.Comment: 5 pages, 4 figures, presented at the NATO Advanced Research Workshop on "Size Dependent Magnetic Scattering", Pecs, Hungary, May 28 - June 1, 200